X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fensemblsequencefetcher.html;fp=help%2Fhtml%2Ffeatures%2Fensemblsequencefetcher.html;h=54b57a33f87a42d8016cfed8b81f6e4a7b5c203a;hb=f3ee64e736d9c83256679e1cfed989d8dd560088;hp=2a62caa0b7ae652c98898f4315016f8cae492747;hpb=a49b953d151391cd9526a7655997c6409f20306c;p=jalview.git diff --git a/help/html/features/ensemblsequencefetcher.html b/help/html/features/ensemblsequencefetcher.html index 2a62caa..54b57a3 100644 --- a/help/html/features/ensemblsequencefetcher.html +++ b/help/html/features/ensemblsequencefetcher.html @@ -25,32 +25,76 @@
Fetching ENSEMBL Data in Jalview -Two types of ENSEMBL source are provided. ENSEMBL queries the - main ENSEMBL site, which only serves data for higher eukaryotes, and - EnsemblGenomes, which provides access to Ensembl Pathogens, and - other warehouses.
-General Use
If you have a set of Ensembl
- peptide or transcript IDs, then you can retrieve them
- via the sequence fetcher dialog opened after selecting the
- most appropriate source (either 'ENSEMBL', or Ensembl Genomes).
- However, Jalview's Ensembl client has a couple of additional
- capabilities:
Retrieving aligned transcripts for a genomic ID -
-If a single genomic identifier is entered in the - Ensembl fetcher, Jalview will return all transcripts and products - for the locus, and display them in a split view - complete with - sequence variant annotation.
-Retrieving orthologs for a gene ID
-If a gene ID is entered (e.g. fox1), Jalview will resolve - Ensembl genomic identifiers for a predefined set of taxa (Mouse, - Rat, Human, Yeast in Jalview 2.10). -
+
+ Two types of ENSEMBL source are provided. ENSEMBL queries the main
+ ENSEMBL warehouse containing data for higher eukaryotes, and
+ EnsemblGenomes, which queries Ensembl Pathogens, and other
+ warehouses.
+ Ensembl support is new in Jalview, and we expect to merge
+ these sources in a future release.
+
+ General Use
If you have a set of Ensembl gene
+ or transcript IDs, then you can retrieve them via the
+ sequence fetcher dialog opened after selecting the most appropriate
+ source (either 'ENSEMBL', or Ensembl Genomes). However, Jalview's
+ Ensembl client has a couple of additional capabilities:
+
+ Retrieving aligned transcripts for a genomic ID +
+If a single genomic identifier is entered in the Ensembl + fetcher, Jalview will return all transcripts and products for the + locus, and display them in a split view - complete with sequence + variant annotation.
++ Retrieving orthologs for a gene ID +
+
+ If a gene ID is entered (e.g. fox1), Jalview will resolve Ensembl
+ genomic identifiers for a predefined set of taxa (Mouse, Rat, Human,
+ Yeast in Jalview 2.10).
+
+ Ensembl Sequence
+ Features
Jalview 2.10 includes support for the
+ visualisation and transfer genomic and transcriptomic sequence
+ features onto protein product sequences. Retrieval of a genomic
+ locus results in a set of transcripts that are annotated with
+ nucleotide variant information and exonic regions. By default,
+ intronic regions will be hidden.
+
+ Variant information on
+ Protein Products
Jalview can translate genomic variant
+ annotation into protein sequence variant codes for variants
+ intersecting coding regions of a gene. To see this in action, use
+ the Calculate→Show cross-references menu to
+ view protein product sequences for the currently displayed (or
+ selected) sequences. The same menu allows you to recover Ensembl
+ exon, transcript and variant information when viewing UniProt
+ sequences.
+
+ Viewing more information about variant annotation
+ Variants are highlighted as red sequence features on the protein
+ sequence, with each one reporting all protein sequence variants
+ observed at that position as a result of the genomic variants.
+ Right-clicking a variant allows you to open the Ensembl Variants web
+ page for each variant, via the Link submenu.
+
+ Work in Progress !
In the next few releases,
+ we hope to improve and extend Jalview's support for working with
+ Ensembl. If you have any problems, questions or suggestions then
+ please get in contact with us via the Jalview discussion list.
+